Related papers: Variable-Order de Bruijn Graphs
We propose a recipe on how to build a general, powerful, scalable (GPS) graph Transformer with linear complexity and state-of-the-art results on a diverse set of benchmarks. Graph Transformers (GTs) have gained popularity in the field of…
Graph data, with its structurally variable nature, represents complex real-world phenomena like chemical compounds, protein structures, and social networks. Traditional Graph Neural Networks (GNNs) primarily utilize the message-passing…
Explainable Graph Neural Networks (GNNs) have been developed and applied to drug-protein binding prediction to identify the key chemical structures in a drug that have active interactions with the target proteins. However, the key…
A skip graph is a resilient application-layer routing structure that supports range queries of distributed k-dimensional data. By sorting deterministic keys into groups based on locally computed random membership vectors, nodes in a…
Covering alignment problems arise from recent developments in genomics; so called pan-genome graphs are replacing reference genomes, and advances in haplotyping enable full content of diploid genomes to be used as basis of sequence…
String kernels are typically used to compare genome-scale sequences whose length makes alignment impractical, yet their computation is based on data structures that are either space-inefficient, or incur large slowdowns. We show that a…
The spectrum of the $k$-power hypergraph of a graph $G$ is called the $k$-ordered spectrum of $G$.If graphs $G_1$ and $G_2$ have same $k$-ordered spectrum for all positive integer $k\geq2$, $G_1$ and $G_2$ are said to be high-ordered…
Branchwidth determines how graphs, and more generally, arbitrary connectivity (basically symmetric and submodular) functions could be decomposed into a tree-like structure by specific cuts. We develop a general framework for designing…
The study of genome rearrangement has many flavours, but they all are somehow tied to edit distances on variations of a multi-graph called the breakpoint graph. We study a weighted 2-break distance on Eulerian 2-edge-colored multi-graphs,…
The paired de Bruijn graph is an extension of de Bruijn graph incorporating mate pair information for genome assembly proposed by Mevdedev et al. However, unlike in an ordinary de Bruijn graph, not every path or cycle in a paired de Bruijn…
Uniform random intersection graphs have received much interest and been used in diverse applications. A uniform random intersection graph with $n$ nodes is constructed as follows: each node selects a set of $K_n$ different items uniformly…
We initiate the algorithmic study of the following "structured augmentation" question: is it possible to increase the connectivity of a given graph G by superposing it with another given graph H? More precisely, graph F is the superposition…
In this paper, we study the ideas of composition and decomposition in the context of vector spaces, graphs and matroids. For vector spaces $\V_{AB},$ treated as collection of row vectors, with specified column set $A\uplus B,$ we define…
A graph has the unique path property UPP_n if there is a unique path of length n between any ordered pair of nodes. This paper reiterates Royle and MacKay's technique for constructing orderly algorithms. We wish to use this technique to…
Temporal graph is an abstraction for modeling dynamic systems that consist of evolving interaction elements. In this paper, we aim to solve an important yet neglected problem -- how to learn information from high-order neighbors in temporal…
Graph Neural Networks (GNNs) are a powerful tool for handling structured graph data and addressing tasks such as node classification, graph classification, and clustering. However, the sparse nature of GNN computation poses new challenges…
We consider large uniform labeled random graphs in different classes with prescribed decorations in their modular decomposition. Our main result is the estimation of the number of copies of every graph as an induced subgraph. As a…
We introduce a variation of the scheduling with precedence constraints problem that has applications to molecular folding and production management. We are given a bipartite graph $H=(B,S)$. Vertices in $B$ are thought of as goods or…
Graphs have been widely used in many applications such as social networks, collaboration networks, and biological networks. One important graph analytics is to explore cohesive subgraphs in a large graph. Among several cohesive subgraphs…
Dujmovi\'c et al (FOCS2019) recently proved that every planar graph $G$ is a subgraph of $H\boxtimes P$, where $\boxtimes$ denotes the strong graph product, $H$ is a graph of treewidth 8 and $P$ is a path. This result has found numerous…